Dunne's exit, which came after an innocuous collision with Stephen Hunt, meant City's already makeshift defence had to reorganise further.
City still created the best chance of the first half, however, and Corluka will be kicking himself for missing it.
The Croat ghosted into the six-yard box to meet Elano's whipped free-kick but the ball bounced up off his knee and flew over the bar.
Reading did threaten when Long headed John Oster's free-kick wide and Matejovsky fired in a bouncing shot that City keeper Joe Hart did well to push away.
But Steve Coppell's side had referee Uriah Rennie to thank when he chose to book Johnson rather than award a penalty before the break when the midfielder seemed to be caught by Ivar Ingimarsson inside the area.
Both teams continued to push forward after the break but, although City had more possession, it was Reading who were attacking with more purpose.
City's defence was stretched when Corluka had to block Doyle's ferocious shot and, from the resulting corner, Hart had to push Bikey's shot on to the bar.
The Royals, however, did not have to wait much longer to break the deadlock.
Marcus Hahnemann's clearance was flicked on by Long and he ran into the box to meet Doyle's pull-back and slot his side in front.
City's response was to throw on Mexican forward Nery Castillo and Ecuador striker Felipe Caicedo to try to salvage something from the match.
They did not lack effort but, in truth, the visitors simply ran out of ideas.
And Reading were able to wrap up the points late on when substitute Kitson ran unchallenged into the box and fired into the bottom corner of the net.
Reading boss Steve Coppell on his side's fight for survival: "We have to accumulate a certain number of points and we cannot relax in any way.
"It is accepted that 40 points is a significant number and I maintain we are capable of getting that, so that is my target.
"We are on a mission to ensure we are in this division again next season."
Manchester City manager Sven-Goran Eriksson: "We have played three games without scoring a goal, and to get one point is not good enough.
"We are not creating chances and, when we do, we are not taking them.
"We are also conceding goals too easily, unlike earlier in the season. It is a difficult time but we have to stick together and come through them."
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